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Related Concept Videos

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Estimating protein function using protein-protein relationships.

Shailesh V Date1

  • 1University of Pennsylvania School of Medicine, Philadelphia, USA.

Methods in Molecular Biology (Clifton, N.J.)
|March 5, 2008
PubMed
Summary
This summary is machine-generated.

Computational functional genomics methods aid in annotating newly identified gene products. Phylogenetic profiling and Rosetta stone linkages help infer protein functions using "guilt-by-association" for genome-wide functional networks.

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Area of Science:

  • Computational biology
  • Genomics
  • Bioinformatics

Background:

  • Characterizing novel gene products is challenging without sequence homology.
  • Functional associations can infer protein functions via the "guilt-by-association" principle.

Purpose of the Study:

  • To describe computational functional genomics methods for protein annotation.
  • To facilitate the assessment of functional linkages between proteins.

Main Methods:

  • Phylogenetic profiling: Measures similarity of protein presence/absence profiles across genomes.
  • Rosetta stone linkages: Identifies fused genes implying functional association between proteins.

Main Results:

  • Both methods enable functional linkage assessment between individual proteins.
  • These approaches can be extended to reconstruct genome-wide functional networks.

Conclusions:

  • Phylogenetic profiling and Rosetta stone linkages are valuable tools for annotating uncharacterized proteins.
  • These methods contribute to understanding genome-wide functional associations and protein networks.